Community Vision Delivery Plan: 2.1 Enabling world-leading environmental research

2 Delivery Plan

2.1 Omics is enabling world-leading environmental research

Omics approaches are being widely used in NERC blue-skies science programmes in addition to being central to several strategic programmes. The underpinning nature of the omics approaches restricts the ability to directly report on its full foot-print within NERC science, however, since all work supported at NBAF exploits omics we can assess those funded applications which exploit NBAF facilities, these have, on average, attracted £50m over 17 awards per annum between 2012-2018 (Figure 1). Highlight Topics (HT), such as ‘eDNA: A Tool for 21st Century Ecology’ have been designed to encourage the development of omics tools within specific areas. Many other HT and science programmes have drawn on omics tools to deliver their objectives with the recent ‘Emerging Risks of Chemicals in the Environment’ drawing on omics to both assess the ecological impact of chemicals by providing high-throughput tools for food-web and community analysis as well as exploiting omics to provide mechanistic impact of chemicals to range of sentinel species. Omics approaches are essential for the delivery of high-quality NERC science. Of the 240 grants applications rated at international competitive (research score of 7 or higher) incorporating omics submitted between 2012-2018 124 (52%) have attached funding. Omics continues to deliver high quality publications outputs showing an above average normalised citation impact when compared to environmental science research generally. Key examples of how omics approaches are being exploited to support NERC delivery plan are provided in Box 1.

While some areas of environmental science have substantial expertise and capacity in omics, others need investment to stimulate activity and ensure NERC science continues to be internationally leading. As our understanding of living systems increases, new directions of research emerge. It is important that novel areas are identified and supported both through discovery science and strategic funding routes.


New insights to fundamental questions: From Fragments to Facts

Ancient DNA: learning from the past

Technological and methodological innovations continue to yield omics data from unprecedented sources, thereby transforming established areas of research. The ability to recover fragments of DNA from archaeological and paleontological material (aDNA) [6] provide insights on evolution of individual species as well as allowing us to reconstruct complete ecosystem (sedimentary ancient DNA – sedaDNA) [7]. These approaches provide a powerful temporal perspective in which to study evolutionary processes (including plant and animal domestication), together with previous climate change events. Archaeogenomics can contextualise and characterise individuals while also allowing us to reconstruct the ecosystems in which they lived. The potential of these techniques is only now being realised, and there remains a vast untapped potential to learn from the past to understand the changing world in which we live. To ensure international leadership, this area requires both targeted infrastructural support as well as development of the skill base to exploit these unique data.

Environmental DNA (eDNA): monitoring ecosystems

The ability to recover fragmented DNA from environmental samples (eDNA) is also having profound impact in understanding ecosystems (examples can be found in special issue of biological conservation 2015 [8]). Applications ranging from non-invasive sampling of organisms through to the reconstruction of food-webs using gut or faecal material is furnishing ecologists and biologists with an unparalleled suite of tools in which to study key communities (special issue Molecular Ecology 2019 [9]). The ability to track individuals, characterise communities and identify the interactions within communities, without requiring direct observation, can transform these disciplines. From assessing population numbers of a species of potentially high conservation risk inhabiting inaccessible terrain to characterising plants visited by specific pollinators, exploitation of omics approaches to deliver answers to previously intractable questions.

Uncovering microbial community biodiversity

Metagenomic approaches are now well-established and provide a valuable tool for studying the structure and function of microbial communities. However, there are significant limitations in studying a homogenised system [10]. A key limitation is the inability to assign functional pathways to a specific microbe or microbial group. With the continual exchange of useful genetic material between bacteria, the mobilome, a systems-level understanding of functional potential of these communities can only be achieved by determining the genetic composition at an individual level [11]. The empowering technology of single cell genomics and transcriptomics is enabling this insight by determining hundreds to thousands of individual microbial genomes [12].

Unlocking Biological ‘Dark matter’: Exploring life

Omics has supported an explosion in our ability to explore biology revealing previously undiscovered organisms (even whole taxa) [13] and demonstrating the functional importance of biomolecules previously thought to unimportant. Global projects focused on microbial content of sea (Global Ocean Sampling Expedition) [14] and land (Earth Microbiome project [15]) continue to reveal new phylogenetic groups as well support novel functional pathways.

As genomics is applied to the full diversity of life it generates a secondary challenge, that of understanding “dark matter” transcriptomics, all those transcripts, which are currently annotated as “unknown” in so many environmental specimens. Developing comparative analysis platforms for sequence data to identify which are species-specific and which are process-specific and the development of tools such as CRISPR-Cas9 for environmental species to unlock these secrets and develop next generation synthetic biology solutions for industry. Unlocking these pathways has significant biotechnological potential. Processes such as mollusc biomineralization which produce incredibly hard and durable materials and where synthetically mimicary of such a natural-processes requires hugely complex technology and lots of energy have the potential to deliver natural products of the future.

Extreme environments as sources of novel compounds for the benefit of society

Microbes are found in the most extreme environments on earth and have found ways to adapt and thrive, from the deep ocean biosphere to volcanic calderas [16]. The majority of these organisms cannot currently be cultured in laboratories, leaving genomics as the primary tool to unlock their extraordinary abilities [13]. Furthermore, natural systems are in a continual arms-race for resources, with this struggle being especially profound in microbial communities [17]. Evolutionary processes have resulted in an array of strategies designed to liberate resources and provide their hosts with a competitive advantage. The succession of fungal and prokaryotic microbes responsible for driving nutrient cycling has have evolved multiple natural product chemistries [18]. Mapping out the chemical ecology underlying these novel pathways and the associated vast array of novel small molecules / secondary metabolites, has significant potential for exploitation within industrial biotechnology. A prime example is that these organisms host a plethora of novel antibiotics as well as providing a reservoir for antimicrobial resistance (AMR) [19].

Disease monitoring in wild populations

The omics tool-kit delivers methods for surveillance of wildlife pathogens (e.g., an ability to unlock life cycles) together with comparative genomic insights into combating these infectious diseases. Pathogens have catastrophic effects on specific populations, together with entire classes of organisms, resulting in impacts to ecosystems globally. For example, white-nose syndrome in North American bats has disrupted trophic cascades, leading to an increase in insect pests [20]; chytrid fungal infection has caused global declines of amphibians[21]; and Hymenoscyphus fraxineus infection resulting in ash dieback has left a major aesthetic mark on the countryside, while devastating associated ecosystems [22]. The emergence of novel diseases within threatened species with small genetic diversity, such as Tasmanian devil facial tumour disease (DFTD), pose significant threats that can lead to extinction [23]. These natural hazards are exacerbated through the interaction with added stressors (e.g., climate change or pollution), resulting in increased pathogenicity. Application of omics technology helps us to better understand what is happening as disease outbreaks occur and also informs strategy for mitigation of their consequences.

Quantifying the World’s biodiversity

The upward trajectory in sequencing capability and capacity shows no sign of slowing. The announcement of a biological ‘moon-shot’, the Earth Biogenome Project (EBP), aimed at unifying the international community behind sequencing every Eukaryotic genome on the planet, is both timely and achievable (https://www.earthbiogenome.org/) [24]. The comparative genomics resource that this initiative will generate will transform evolutionary biology, while having untold benefits in all areas of science. From application, such as providing templates for synthetic biology, to fundamental understanding of evolutionary process, the EBP will change our understanding of every living system. The UK component of the project, provisionally entitled ‘The Darwin Tree of Life Project’ (https://www.sanger.ac.uk/news/view/genetic-code-66000-uk-species-be-sequenced), will have a primary focus on sequencing species from the British Isles and UK protectorates. Linked to this will be a focus around key observatories (e.g. St Kilda, Priests Pot and Wytham Woods), yielding immediate value-added benefits by complementing conventional long-term datasets. Significant uplift can be achieved by strategically adding to resources with selected re-sequencing detailed studies to investigate the relationship between genome architecture and a changing environment.

Genotype-environment interactions in wild species

Understanding how the environment helps shape phenotype has been significantly enhanced through multi-omics analysis [25], which allows us to characterise genome architecture, epigenetic modifications (miRNA, DNA methylation and histone modifications), transcriptomics and associated microbial communities. Unravelling the causative relationships that link environmental changes through alterations at the level of genome, epigenome and transcriptome with the phenotype, represents a significant challenge for integrative biosciences. Exploiting Omics for examining adaptive and acclimative processes will allow us to model evolutionary trajectories predicting resilience of individuals, populations and ecosystem to global change events.
Understanding community relationships

Many organisms share intermittent interactions: some being one-way dependencies (e.g. parasitism); some interactions are mutually beneficial, to such a degree that the partners have become interdependent (e.g. lichens); while others have less closely coupled relationships (e.g. microbiomes or rhizosphere interactions) where benefits are derived but not essential (commensalism). Omics approaches are enabling us to dissect symbiosis in all of its forms [26], characterising the relationships, benefits, co-dependencies and co-evolutionary processes that may be involved. Critical interaction support some of the most iconic ecosystems such as marine reefs which really on the interaction between coral and their algal symbiosis, an interaction that is under specific pressure given global warming [27]. These complex interactions extend our understanding into how complex communities interact to yield sustainable ecosystems. This is especially pertinent to soils, where the rhizosphere represents interactions between plant, microbe (bacteria & fungal) and macro/micro invertebrates and that maintain sustainable terrestrial environments by supporting natural and agricultural ecosystems [28]. The excitement that surrounds the more loosely coupled interactions, such as the microbiome and the rhizosphere, is that we can dissect and even manipulate the composition of these communities to combat pollution or engineer a more resilient host/ecosystem.

Pollution and environmental health

A recent analysis revealed that 16% of global human deaths are linked to pollution, and our ecosystems are at no less risk [29]. Biomes delivering essential ecosystem services are being assailed by cocktails of synthetic chemicals in the form of agrochemicals, industrial chemicals, consumer products, pharmaceuticals and veterinary medicines, all of which reach our green and blue spaces in significant amounts. Added to this are various particles and gases in the air, the by-products from the combustion of waste products. Pollutants range from these atmospheric contaminates to the visible and invisible plastics in our soils, rivers and seas. A complex array of legislation attempts to protect both human health and ecosystems from the effects of pollution, but it has two significant shortfalls. Firstly, evidence is generated on single compounds under largely laboratory conditions and secondly only a small number of representative organisms are tested. These limitations are partially addressed by applying safety margins to compensate for differential species sensitivities, mixture effects, changes between laboratory and field conditions and longer exposure durations in the real world. Application of omics technologies, combined with a comparative mechanistic understanding of biological systems, has the potential to detect the full spectrum of pollutants in our environments identify the associated changes and hence generate predictive frameworks that can more accurately identify risks to both human health and ecosystems for species with different physiologies. These novel approaches together represent a vision of Precision Environmental Health [30].

Towards real time monitoring

The combination between microfluidics and nanopore sequencing provides the realistic future possibility for field omics analysis and real-time automatic genomics monitoring of the environment. These tools may benefit research where field-based analysis will dynamically informing monitoring regimes, but they are also important to support human and environmental protection. For example current microbiological test for beach-waters take 48 hours and exclude viral load, issue that can be addressed given development in sampling and sequencing technologies. However, data streams containing such information provided challenges demand develops in artificial Intelligence or neural networks to interpret the real time change to provide human accessible monitoring information.